Question: DESeq2 load failed for Bioconductor ver 3.9
0
gravatar for biancaineshoch
9 weeks ago by
biancaineshoch0 wrote:

Hello all.

I'm currently having issues loading DESeq2 into R version 3.6. I upgraded Bioconductor from version 3.7 to the latest version, 3.9. I am using my school's server to conduct RNA-Seq analysis.

Here is the error message that I receive:

> library(DESeq2)
Error: package or namespace load failed for ‘DESeq2’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
 there is no package called ‘Hmisc’
In addition: Warning message:
replacing previous import ‘Biobase::dims’ by ‘BiocGenerics::dims’ when loading ‘DESeq2’

Here is the sessionInfo():

> sessionInfo()
R version 3.6.0 (2019-04-26)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.6 LTS

Matrix products: default
BLAS:   /usr/lib/libblas/libblas.so.3.6.0
LAPACK: /usr/lib/lapack/liblapack.so.3.6.0

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] parallel  stats4    stats     graphics  grDevices utils     datasets
[8] methods   base

other attached packages:
 [1] org.Hs.eg.db_3.8.2
 [2] PoiClaClu_1.0.2.1
 [3] RColorBrewer_1.1-2
 [4] pheatmap_1.0.12
 [5] GenomicAlignments_1.16.0
 [6] TxDb.Hsapiens.UCSC.hg38.knownGene_3.4.6
 [7] GenomicFeatures_1.36.0
 [8] AnnotationDbi_1.46.0
 [9] stringr_1.4.0
[10] stringi_1.4.3
[11] Rsamtools_1.32.3
[12] Biostrings_2.48.0
[13] XVector_0.20.0
[14] SummarizedExperiment_1.10.1
[15] DelayedArray_0.6.6
[16] BiocParallel_1.14.2
[17] matrixStats_0.54.0
[18] Biobase_2.40.0
[19] GenomicRanges_1.32.7
[20] GenomeInfoDb_1.20.0
[21] IRanges_2.14.12
[22] S4Vectors_0.18.3
[23] BiocGenerics_0.30.0

loaded via a namespace (and not attached):
 [1] progress_1.2.1         lattice_0.20-38        colorspace_1.4-1
 [4] rtracklayer_1.40.6     blob_1.1.1             XML_3.98-1.19
 [7] rlang_0.3.4            DBI_1.0.0              bit64_0.9-7
[10] GenomeInfoDbData_1.2.1 zlibbioc_1.26.0        munsell_0.5.0
[13] gtable_0.3.0           memoise_1.1.0          biomaRt_2.40.0
[16] Rcpp_1.0.1             xtable_1.8-4           scales_1.0.0
[19] BiocManager_1.30.4     annotate_1.62.0        bit_1.1-14
[22] hms_0.4.2              digest_0.6.18          grid_3.6.0
[25] tools_3.6.0            bitops_1.0-6           magrittr_1.5
[28] RCurl_1.95-4.12        RSQLite_2.1.1          crayon_1.3.4
[31] pkgconfig_2.0.2        Matrix_1.2-17          prettyunits_1.0.2
[34] assertthat_0.2.1       httr_1.4.0             R6_2.4.0
[37] compiler_3.6.0
deseq2 • 148 views
ADD COMMENTlink modified 9 weeks ago by Martin Morgan ♦♦ 23k • written 9 weeks ago by biancaineshoch0
Answer: DESeq2 load failed for Bioconductor ver 3.9
0
gravatar for Michael Love
9 weeks ago by
Michael Love24k
United States
Michael Love24k wrote:

DESeq2 depends on Hmisc, so that is the main problem here.

What happens when you try to install DESeq2:

BiocManager::install("DESeq2")

If you do not have permissions, you may have to ask an administrator to reinstall for you.

ADD COMMENTlink written 9 weeks ago by Michael Love24k

Thank you for your quick reply! My PI has root access and got a similar error, so I'm not sure my problem is permissions. The entire output stream is too long for me to include, so I cut to the first fatal error. Here is the result of installing DESeq2:

> > BiocManager::install("DESeq2") Bioconductor version 3.9 (BiocManager 1.30.4), R 3.6.0 (2019-04-26) Installing package(s) 'DESeq2' also installing the dependencies ‘vctrs’, ‘pillar’, ‘tibble’, ‘viridis’,
> ‘ggplot2’, ‘Hmisc’ trying URL
> 'https://cloud.r-project.org/src/contrib/vctrs_0.1.0.tar.gz' Content
> type 'application/x-gzip' length 412633 bytes (402 KB)
> ================================================== downloaded 402 KB trying URL
> 'https://cloud.r-project.org/src/contrib/Hmisc_4.2-0.tar.gz' Content
> type 'application/x-gzip' length 732731 bytes (715 KB)
> ================================================== downloaded 715 KB trying URL
> 'https://bioconductor.org/packages/3.9/bioc/src/contrib/DESeq2_1.24.0.tar.gz'
> Content type 'application/x-gzip' length 2056901 bytes (2.0 MB)
> ================================================== downloaded 2.0 MB
> * installing *source* package ‘vctrs’ ...
> ** package ‘vctrs’ successfully unpacked and MD5 sums checked
> ** using staged installation
> ** libs gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG     -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c compare.c -o compare.o In file included from vctrs.h:2:0,
>                  from compare.c:1: /usr/share/R/include/R.h:55:80: fatal error: stdlib.h: No such file or directory compilation
> terminated. /usr/lib/R/etc/Makeconf:167: recipe for target 'compare.o'
> failed make: *** [compare.o] Error 1 ERROR: compilation failed for
> package ‘vctrs’
> * removing ‘/home/bih1/R/x86_64-pc-linux-gnu-library/3.6/vctrs’ ERROR: dependency ‘vctrs’ is not available for package ‘pillar’
> * removing ‘/home/bih1/R/x86_64-pc-linux-gnu-library/3.6/pillar’ ERROR: dependency ‘pillar’ is not available for package ‘tibble’
> * removing ‘/home/bih1/R/x86_64-pc-linux-gnu-library/3.6/tibble’ ERROR: dependency ‘tibble’ is not available for package ‘ggplot2’
> * removing ‘/home/bih1/R/x86_64-pc-linux-gnu-library/3.6/ggplot2’ ERROR: dependency ‘ggplot2’ is not available for package ‘viridis’
> * removing ‘/home/bih1/R/x86_64-pc-linux-gnu-library/3.6/viridis’ ERROR: dependencies ‘ggplot2’, ‘viridis’ are not available for package
> ‘Hmisc’
> * removing ‘/home/bih1/R/x86_64-pc-linux-gnu-library/3.6/Hmisc’ ERROR: dependencies ‘ggplot2’, ‘Hmisc’ are not available for package ‘DESeq2’
> * removing ‘/home/bih1/R/x86_64-pc-linux-gnu-library/3.6/DESeq2’ The downloaded source packages are in
>         ‘/tmp/RtmpfDJ5u3/downloaded_packages’ installation path not writeable, unable to update packages: acepack, ade4,   affy, affyio,
> askpass, backports, base64enc, bdsmatrix, bibtex, bindrcpp,   Biobase,
> BiocParallel, Biostrings, bit, bit64, bitops, car, caTools,  
> checkmate, colorspace, covr, curl, data.table, DelayedArray, deldir,
> diffobj,   digest, ellipsis, fansi, fastmatch, FNN, freetypeharfbuzz,
> fs, gdtools, gee,   GenomicAlignments, GenomicRanges, git2r, glue,
> kernlab, ks, later, lazyeval, leaps,   openxlsx, pcaMethods, pkgload,
> plyr, png, polysat, preprocessCore, pROC,   reshape2, reticulate, rgl,
> rlang, Rmpi, RSQLite, rtracklayer, Rwave,   SummarizedExperiment,
> edgeR, effects, expm, irlba, lme4, lmtest, locfit, maptools,  
> foreign, genefilter, GOstats, graph, gss, KernSmooth, lattice, MASS,
> Matrix,   RcppParallel, Rgraphviz, rmutil, spatial, stable, statip,
> survival, sva 

> Warning messages: 1: In install.packages(pkgs = doing,
> lib = lib, repos = repos, ...) :   installation of package ‘vctrs’ had
> non-zero exit status 2: In install.packages(pkgs = doing, lib = lib,
> repos = repos, ...) :   installation of package ‘pillar’ had non-zero
> exit status 3: In install.packages(pkgs = doing, lib = lib, repos =
> repos, ...) :   installation of package ‘tibble’ had non-zero exit
> status 4: In install.packages(pkgs = doing, lib = lib, repos = repos,
> ...) :   installation of package ‘ggplot2’ had non-zero exit status 5:
> In install.packages(pkgs = doing, lib = lib, repos = repos, ...) :  
> installation of package ‘viridis’ had non-zero exit status 6: In
> install.packages(pkgs = doing, lib = lib, repos = repos, ...) :  
> installation of package ‘Hmisc’ had non-zero exit status 7: In
> install.packages(pkgs = doing, lib = lib, repos = repos, ...) :  
> installation of package ‘DESeq2’ had non-zero exit status
ADD REPLYlink modified 9 weeks ago • written 9 weeks ago by biancaineshoch0

Looks like the problem starts with vctrs:

fatal error: stdlib.h: No such file or directory compilation terminated. /usr/lib/R/etc/Makeconf:167: recipe for target 'compare.o' failed make: * [compare.o] Error 1 ERROR: compilation failed for package ‘vctrs’

Not sure how you could fix on your system...

DESeq2 install fine on Ubuntu for many users I know (myself included).

ADD REPLYlink written 9 weeks ago by Michael Love24k

Hmm. I'll continue to troubleshoot then. Thanks for your help, I'm a big fan of your work.

ADD REPLYlink written 9 weeks ago by biancaineshoch0

Hmm. I'll continue to troubleshoot then. Thanks for your help, I'm a big fan of your work.

ADD REPLYlink written 9 weeks ago by biancaineshoch0

My guess is that you have updated your OS or compilers after installing R, and the best bet would be to re-install R. Also simplify the problem to tackling the first failure -- BiocManager::install("vctrs")

ADD REPLYlink written 9 weeks ago by Martin Morgan ♦♦ 23k
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